inst/NEWS.md

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

CHANGES IN VERSION 2.18.1

(GitHub master branch)

BUG FIXES

• Handle missing NAs while sub-setting for ranges. Issue: 1013
• Better error handling when zero mutated samples are encountered in clinicalEnrichment. Issue: 1010
• MAJOR: read.maf by default coerces clinical data columns to character. This bug fix avoids it and is auto detected. Issue: 997

ENHANCEMENTS

• Better sorting of oncoplot with collapsePathway
• Changed default background for oncoplot from gray to #ecf0f1
• Changed default signature database to SBS_v3.4 (from legacy)
• Update tmb function

NEW FUNCTIONS

• gisticCompare() for comparing two GISTIC objects

CHANGES IN VERSION 2.18.0

(Bioconductor release branch)

NEW FUNCTIONS

• pathways and plotPathwaysfor summarizing & visualizing pathways Issue: 956
• coGisticChromPlot for plotting two GISTIC objects side-by-side. PR by biosunsci 954
• readGistic can take gistic output directory as an input. PR by biosunsci 954

BUG FIXES

• Bug fixes while processing custom pathways
• Bug fix in oncoplot for drawing borders. 958
• Bug fix in plotSignatures for hardcoded axis limits. 949
• Bug fix in mafSurvival legend when samples argument is give. 937
• Bug fix in subsetMaf while handling only CNV events. 908
• Error handling when no deep/shallow CNV events found. 899
• Bug fix in oncoplot for duplicated values in gene list. 889

ENHANCEMENTS

• Added argument collapsePathway to oncoplot. Issue: 956
• Improved annovarToMaf with better handling of indels and Variant_Type. Issue: 940
• Include absolute contribution of each signature in extractSignatures output. Issue: 939
• Added tsbToPIDs for custom names in oncoplot. Issue: Issue: 936
• Added DSEL protein to the database. Issue: 933
• Added MUC3A protein to the database. Issue: 932
• Added showOnlyPathway argument to oncoplot
• Added pathdb argument to PlotOncogenicPathways. Issue: 923
• Emit warnings when fishers test can not be performed during somaticInteractions. Issue: 921
• Added leftMar and topMar arguments to somaticInteractions. Issue: 913
• Added toptBarLims argument to oncoplot. Issue: 910
• Added data argument to lollipopPlot function. Issue: 894
• Added sortByM1 and sortByM2 argument to coOncoplot. Issue: 888
• Added arguments leftBarVline, leftBarVlineCol, rightBarVline, rightBarVlineCol topBarHline topBarHlineCol to oncoplot. Issue: 874
• Added revPal argument to somaticInteractions. Issue: 859
• Fix legend and color codes for numeric annotations in oncoplot. Issue: 363

CHANGES IN VERSION 2.16.0

(Bioconductor release version)

• No changes

CHANGES IN VERSION 2.14.0

• No changes

CHANGES IN VERSION 2.12.05

BUG FIXES

• genes parameter in plotClusters can't accept list of genes. Issue: 828
• Ignore NAs while generating trinucleotideMatrix. Issue: 841

ENHANCEMENTS

• Added protein structure for NRIP1. Issue: 832
• Added protein structure for SETBP1. Issue: 696

CHANGES IN VERSION 2.12.00

(BC 3.15)

NEW FUNCTIONS

• gtMarkers, prepAscat, prepAscat_t, segmentLogR provides interface to copy number analysis with ASCAT.
• plotMosdepth and plotMosdepth_t processes output generated by Mosdepth and performs copy number analysis with DNAcopy
• cancerhotspotsAggr Aggregates cancerhotspots reports

ENHANCEMENTS

• Added support for plotting adjusted p-values in somaticInteractions. Issue: 813
• Added support for the protein structure BECN2 Issue: 696

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.